I used to work in the independent games industry. In 2004, I designed and wrote a little Action-Puzzle game titled Drop! (feel free to look it up on GameFaqs). We sold it in stores for $10, and online for $5, however, we got $.33 per retail copy sold (blame publishers) vs. $2.50 or so per online copy sold. We sold a few hundred thousand copies or so at retail across a 6 month period (#4 for sales for a couple months, but no one pays attention to jewel case games).
Here's the trick: the online version had an online high-score system. You could play the online copy for free, but you didn't get access to the shared high-score system unless you bought it. We sold less than 100 copies online, but saw several hundred thousand unique IP addresses hit the high score system every day (and this kept up for years, not just people "trying out the high score system").
For 6 months of work, I made about $30,000 on that (a couple other guys made similar amounts), which eventually didn't justify the effort - because people who want to play a game don't care about making it possible for the creators to keep making games.
I work for Microsoft now :P